Introduction
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Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.

Examples
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* Convert FASTQ to FASTA:

        seqtk seq -a in.fq.gz > out.fa

* Convert ILLUMINA 1.3+ FASTQ to FASTA and mask bases with quality lower than 20 to lowercases (the 1st command line) or to `N` (the 2nd):

        seqtk seq -aQ64 -q20 in.fq > out.fa
        seqtk seq -aQ64 -q20 -n N in.fq > out.fa

* Fold long FASTA/Q lines and remove FASTA/Q comments:

        seqtk seq -Cl60 in.fa > out.fa

* Convert multi-line FASTQ to 4-line FASTQ:

        seqtk seq -l0 in.fq > out.fq

* Reverse complement FASTA/Q:

        seqtk seq -r in.fq > out.fq

* Extract sequences with names in file `name.lst`, one sequence name per line:

        seqtk subseq in.fq name.lst > out.fq

* Extract sequences in regions contained in file `reg.bed`:

        seqtk subseq in.fa reg.bed > out.fa

* Mask regions in `reg.bed` to lowercases:

        seqtk seq -M reg.bed in.fa > out.fa

* Subsample 10000 read pairs from two large paired FASTQ files (remember to use the same random seed to keep pairing):

        seqtk sample -s100 read1.fq 10000 > sub1.fq
        seqtk sample -s100 read2.fq 10000 > sub2.fq

* Trim low-quality bases from both ends using the Phred algorithm:

        seqtk trimfq in.fq > out.fq

* Trim 5bp from the left end of each read and 10bp from the right end:

        seqtk trimfq -b 5 -e 10 in.fa > out.fa
